Community-level dormancy potential regulates bacterial beta-diversity succession during the co-composting of manure and crop residues

The measurement and insight of bacterial community structure succession in cyanobacteria biochar co-composting based on basic carbon and nitrogen indices

The effects of cyanobacteria biochar (CB) amendment on microbial community succession (MCS) during pig manure co-composting was evaluated. Conventional composting (T1) and different concentrations of CB co-composting were set up here (T2: 2.5% CB, T3: 5% CB, T4: 7.5% CB, T5: 10% CB, and T6: 20% CB). Core substrate indicators and microbial information were used to gain insight into microbial community succession structure (MCSS) by CB treatments. Low concentrations of CB show higher organic degradation rates (2.4% vs 2.2%; and Y = C ∗(1- e(-k∗x))), while high concentrations increased the content of TKN (T5: 54.40%). An innovative diversity quantization method (pan-γ-diversity T5:42.275, T1: 40.642, and T2: 34.285) was proposed through linear simulation and integration. CB optimized Bacillus and Thermobacillus were key organic degradation genera during succession (collaborate with Caldicoprobacter) and increased the abundance of important nitrogen fixation genera Chelativorans (Day 42: minimun 4.8 times; and Day 72: minimum 1.3 times) and Longispora (Max 10.0%). The existence of bacteria Caldicoprobacter (2.0-9.3%) on mineralization process showed the synergy and co-assembly effects of CB on MCSS. Moreover, mantel test also shows the assembled and cooperation of Firmicutes and Actinobacteria.

Impact of aeration rate on the transfer range of antibiotic-resistant plasmids during manure composting

Conjugative plasmids are important vectors of mobile antibiotic resvistance genes (ARGs), facilitating their horizontal transfer within the environment. While composting is recognized as an effective method to reduce antibiotics and ARGs in animal manure, its impact on the bacterial host communities containing antibiotic-resistant plasmids remains unclear. In this study, we investigated the permissiveness of bacterial community during composting when challenged with multidrug-resistant conjugative RP4 plasmids, employing Pseudomonas putida as the donor strain. Ultimately, this represents the first exploration of the effects of aeration rates on the range of RP4 plasmid transfer hosts. Transconjugants were analyzed through fluorescent reporter gene-based fluorescence-activated cell sorting and Illumina sequencing. Overall, aeration rates were found to influence various physicochemical parameters of compost, including temperature, pH, total organic matter, total nitrogen, and potassium. Regarding RP4 plasmid host bacteria, the dominant phylum was determined to shift from Bacteroidetes in the raw material to Proteobacteria in the compost. Notably, a moderate-intensity aeration rate (0.05 L/min/L) was found to be more effective in reducing the diversity and richness of the RP4 plasmid host bacterial community. Following composting, the total percentage of dominant transconjugant-related genera decreased by 66.15-76.62%. Ultimately, this study determined that the aeration rate negatively impacts RP4 plasmid host abundance primarily through alterations to the environmental factors during composting. In summary, these findings enhance our understanding of plasmid host bacterial communities under varying composting aeration rates and offer novel insights into preventing the dissemination of ARGs from animal manure to farmland.

Potassium persulfate enhances humification of chicken manure and straw composting: The perspective of rare and abundant microbial community structure and ecological interactions

Improper disposal of organic solid waste results in serious environmental pollution. Aerobic composting provides an environmentally friendly treatment method, but improving humification of raw materials remains a challenge. This study revealed the effect of different concentrations of potassium persulfate (PP) on humification of chicken manure and straw aerobic composting and the underlying microbial mechanisms. The results showed that when 0.6 % PP was added (PPH group), humus and the degree of polymerization were 80.77 mg/g and 2.52, respectively, which were significantly higher than those in 0.3 % PP (PPL group). As the concentration of PP was increased, the composition of rare taxa (RT) changed and improved in evenness, while abundant taxa (AT) was unaffected. Additionally, the density (0.037), edges (3278), and average degree (15.21) in the co-occurrence network decreased compared to PPL, while the average path (4.021) and modularity increased in PPH. This resulted in facilitating the turnover of matter, information, and energy among the microbes. Interestingly, cooperative behavior between microorganisms during the maturation period (24-60 d) occurred in PPH, but competitive relationships dominated in PPL. Cooperative behavior was positively correlated with humus (p < 0.05). Because the indices, such as higher degree, betweenness centrality, eigenvector centrality, and closeness centrality of the AT, were located in the microbial network center compared to RT, they were unaffected by the concentration of PP. The abundance of carbohydrate and amino acid metabolic pathways, which play an important role in humification, were higher in PPH. These findings contribute to understanding the relative importance of composition, interactions, and metabolic functionality of RT and AT on humification during chicken manure and straw aerobic composting under different concentrations of PP, as well as provide a basic reference for use of various conditioning agents to promote humification of organic solid waste.

Risk level and removal performance of antibiotic resistance genes and bacterial pathogens in static composting with different temperatures

The effect of different levels of temperature on resistance genes is not clear in mesophilic static composting (<50 °C). This study conducted livestock manure composting with different temperature gradients from 20 to 50 °C, it was found that the reduction rates of risk rank-I antibiotic resistance genes (from 3 % to 66 %), metal resistance genes (from -50 % to 76 %) and bacterial pathogens (from 72 % to 91 %) all increased significantly with increasing temperature from 20 to 50°C. The vulnerability of bacterial communities increased significantly, and the assembly process of bacterial communities changed from deterministic to stochastic with the increase of composting temperature. Higher temperature could accelerate the removal of thermolabile resistance genes hosts or pathogenic hosts carrying mobile genetic elements by directly or indirectly affecting organic acids content. Therefore, for soil safety, the temperature of the manure recycling process should be increased as much as possible.

Microbe-aided thermophilic composting accelerates manure fermentation

Aerobic composting is a key strategy to the sustainable use of livestock manure, which is however constrained by the slow kinetics. Microbe-aided thermophilic composting provides an attractive solution to this problem. In this study, we identified key thermophilic bacteria capable of accelerating manure composting based on the deciphering of manure bacterial community evolution in a thermophilic system. High-throughput sequencing showed a significant evolution of manure bacterial community structure with the increasing heating temperature. Firmicutes were substantially enriched by the heating, particularly some known thermotolerant bacterial species, such as Novibacillus thermophiles, Bacillus thermolactis, and Ammoniibacillus agariperforans. Correspondingly, through function prediction, we found bacterial taxa with cellulolytic and xylanolytic activities were significantly higher in the thermophilic process relative to the initial stage. Subsequently, a total of 47 bacteria were isolated in situ and their phylogenetic affiliation and degradation capacity were determined. Three isolates were back inoculated to the manure, resulting in shortened composting process from 5 to 3 days with Germination Index increased up to 134%, and improved compost quality particularly in wheat growth promoting. Comparing to the mesophilic and thermophilic Bacillus, the genomes of the three isolates manifested some features similar to the thermophiles, including smaller genome size and mutation of specific genes that enhance heat tolerance. This study provide robust evidence that microbe-aided thermophilic composting is capable to accelerate manure composting and improve the quality of compost, which represents a new hope to the sustainable use of manure from the meat industry.

Effect of initial moisture content, resulting from different ratios of vegetable waste to maize straw, on compost was mediated by composting temperatures and microbial communities at low temperatures

Owing to the huge amounts and perishable character of vegetable wastes, composting is one of the best options for recycling vegetable wastes post-harvest. The initial moisture content (MC) is critical for optimizing composting process, but the effect of high MC in undehydrated vegetable wastes on composting was rarely reported. For this, the plant-scale windrows were prepared by mixing cauliflower waste and maize straw at different ratios to control initial MC of 70 % (T1-70) and 80 % (T2-80), respectively, and composted in winter. As composting progressed, substantial organic matter degradation, progressive humification, decreases in electrical conductivity and increases of pH and germination index (GI) were observed in both treatments. Nonetheless, T1-70 accelerated heating rate early during composting, prolonged high temperature period (>50 °C) by 30 d, thus increased the harmless level of composting, and significantly improved the humification of end-products compared to T2-80. Results also revealed that T1-70 activated more indigenous microbes and enhanced microbial interactions early during composting, with the fungi enriched in T1-70 playing an important role in accelerating the composting process. Remarkably, the difference in composting temperatures, humification degree, and microbial communities between the two treatments was most significant during the maturation phase. In this phase, MWH_CFBk5, Planktosalinus, Pseudopedobacter, and Luteimonas enriched in T1-70 were positively correlated with humification indices. It is suggested that the effect of initial MC, resulting from different ratios of vegetable waste to maize straw, on their composting was mediated by the composting temperature and microbial communities at low temperatures.

Integrating bioprocess and metagenomics studies to enhance humic acid production from rice straw

Rice straw burning annually (millions of tons) leads to greenhouse gas emissions, and an alternative solution is producing humic acid with high added-value. This study aimed to examine the influence of a microbial consortium and other additives (chicken manure, urea, olive mill waste, zeolite, and biochar) on the composting process of rice straw and the subsequent production of humic acid. Results showed that among the fungal species, Thermoascus aurantiacus exhibited the most prominent impact in expediting maturation and improving compost quality, and Bacillus subtilis was the most abundant bacterial species based on metagenomics analysis. The highest temperature, C/N ratio reduction, and amount of humic acid production (Respectively in lab 61 °C, 54.67%, 298 g kg-1 and in pilot level 65 °C, 72.11%, 310 g kg-1) were related to treatments containing these microorganisms and other additives except urea. Consequently, T. aurantiacus and B. subtilis can be employed on an industrial scale as compost additives to further elevate quality. Functional analysis showed that the bacterial enzymes in the treatments had the highest metabolic activities, including carbohydrate and amino acid metabolism compared to the control. The maximum enzymatic activities were in the thermophilic phase in treatments which were significantly higher than that in the control. The research emphasizes the importance of identifying and incorporating enzymatically active strains that are suitable for temperature conditions, alongside the native strains in decomposing materials. This strategy significantly improves the composting process and yields high-quality humic acid during the thermophilic phase.

Responses of microorganisms to different wavelengths of light radiation during green waste composting

Light radiation can degrade recalcitrant materials like lignocelluloses in litter and serve as a physical condition to accelerate green waste (GW) decomposition, but few studies have considered the microbial effects of light wavelength on GW composting. This study innovatively investigated the effects of different wavelengths of light radiation, including full-spectrum, no blue light, no UV, no UV-A, no UV-B, and dark conditions, on accelerating the GW composting process. Especially, the study explored the dynamic changes in the degradation of lignocelluloses and evaluated the responses of microorganisms throughout the composting process under different light radiation wavelengths. No blue light (where radiation between 400 and 500 nm was blocked by the film) yielded the highest-quality compost within 40 days. In comparison to the dark (control), no blue light exhibited an elevated composting temperature (56.7 °C), an extended thermophilic phase (6 days), and increased degradation rates of lignin, cellulose, and hemicellulose by 13 %, 15 %, and 12 %, respectively. This study revealed that during the composting mesophilic phase, bacterial diversity performed best under no blue light, while fungal diversity excelled under full-spectrum. In the thermophilic phase, microbial diversity exhibited optimal performance under full-spectrum. During the cooling phase, bacterial diversity was highest under no blue light, and fungal diversity excelled under no UV-A. During the mesophilic and cooling phases, the bacterial ACE index for no blue light exceeded that of the other light radiation wavelengths, with values of 418 and 494, respectively. Under no blue light, the Shannon index of microorganisms remained within the range of 2.0-4.8, demonstrating superior performance. Meanwhile, the relative abundances of lignin-degrading microorganisms (Flavobacterium, Acaulium, and Acremoniu) under no blue light has increased, demonstrating improved microbial community structures. Therefore, no blue light radiation offered a novel approach to expedite GW composting.

Biodiversity and core microbiota of key-stone ecological clusters regulate compost maturity during cow-dung-driven composting

The primary objectives of this study were to explore the community-level succession of bacteria, fungi, and protists during cow-dung-driven composting and to elucidate the contribution of the biodiversity and core microbiota of key-stone microbial clusters on compost maturity. Herein, we used high-throughput sequencing, polytrophic ecological networks, and statistical models to visualize our hypothesis. The results showed significant differences in the richness, phylogenetic diversity, and community composition of bacteria, fungi, and eukaryotes at different composting stages. The ASV191 (Sphingobacterium), ASV2243 (Galibacter), ASV206 (Galibacter), and ASV62 (Firmicutes) were the core microbiota of key-stone bacterial clusters relating to compost maturity; And the ASV356 (Chytridiomycota), ASV470 (Basidiomycota), and ASV299 (Ciliophora) were the core microbiota of key-stone eukaryotic clusters relating to compost maturity based on the data of this study. Compared with the fungal taxa, the biodiversity and core microbiota of key-stone bacterial and eukaryotic clusters contributed more to compost maturity and could largely predict the change in the compost maturity. Structural equation modeling revealed that the biodiversity of total microbial communities and the biodiversity and core microbiota of the key-stone microbial clusters in the compost directly and indirectly regulated compost maturity by influencing nutrient availability (e.g., NH4+-N and NO3--N), hemicellulose, humic acid content, and fulvic acid content, respectively. These results contribute to our understanding of the biodiversity and core microbiota of key-stone microbial clusters in compost to improve the performance and efficiency of cow-dung-driven composting.

A review of the definition, influencing factors, and mechanisms of rapid composting of organic waste

Composting is a traditional method of treating organic waste. A growing number of studies have been focusing on accelerating the process to achieve "rapid composting." However, the specific definition and influencing factors of rapid composting remain unclear. Therefore, we aimed to gather more insight into the features of rapid composting by reviewing the literature concerning organic waste composting published in the Web of Science database in the past 5 years. We selected 1615 sample studies with "composting" as the subject word and analyzed the effective composting time stated in each study. We defined rapid composting within 15 days using the median test and quartile method. Based on this definition, we summarized the influencing factors of "rapid composting," namely materials, reactors, temperature, and microorganisms. Finally, we summarized two mechanisms related to humus formation during organic waste rapid composting: high temperature-promoting maturation and microbial driving mechanisms. This literature review compiled useful references to help promote the development of rapid composting technology and related equipment.

Inoculating exogenous bacterium Brevibacillus laterosporus ZR-11 at maturity stage accelerates composting maturation by regulating physicochemical parameters and indigenous bacterial community succession

Brevibacillus laterosporus ZR-11, a bio-control strain, was innovatively inoculated at maturity stage of composting to clarify its effect on physicochemical parameters and indigenous bacterial community structure in compost pile. Results revealed that ZR-11 inoculum rapidly increased pile temperature to 52 ºC and raised germination index (GI) value to beyond 85% on day 3, thereby achieving higher pile temperature and GI in the inoculated group than the non-inoculated group almost along maturity stage, and also decreased C/N ratio of the inoculated group to below 20 by composting end (day 8). Also, ZR-11 succeeded in colonizing compost pile along maturity stage. These suggested that ZR-11 as inoculum at maturity stage could accelerate compost maturation and have a potential to participate in bio-fertilizer production. High-throughput sequencing indicated that bacterial community structure experienced substantial succession in the inoculated and non-inoculated groups, and Firmicutes, Proteobacteria, and Actinobacteria were the dominant phyla in the two groups during maturity stage, with their abundances higher in the inoculated group. Saccharomonospora and Ammoniibacillus abundance increased on day 3 while Actinomadura abundance increased on day 6 in the inoculated group. As verified statistically, pile temperature and pH were key factors closely linked to dominant genera abundance, where Saccharomonospora and Ammoniibacillus abundance were positively correlated to pile temperature, while Actinomadura abundance was positively correlated to pile pH. Thus, it was inferred that ZR-11 inoculum could improve parameters such as temperature and pH to modify dominant genera abundance, thus regulating indigenous bacterial community succession, which might in turn promote compost maturation.

Multi-omics study of sulfur metabolism affecting functional microbial community succession during aerobic solid-state fermentation

Microbial-mediated sulfur metabolism is closely related to carbon and nitrogen metabolism in natural biological systems. In this study, the effects of sulfur metabolism on microbial communities and functional enzyme succession were investigated based on integrated multi-omics by adding sulfur-containing compounds to aerobic fermentation systems. Sulfur powder was oxidized to S2O32- and subsequently to SO42- by the microbial sulfur-oxidizing system, which lowered the pH to 7.5 on day 7. The decrease in pH resulted in Planifilum (secreted S8, M17 and M32 proteases) losing its competitive advantage, whereas Novibacillus (secreted M14 and M19 metalloproteases) became dominant. Structural proteomics indicated that the surface of Novibacillus proteases has more negatively charged amino acid residues that help maintain protein stability at low pH. These findings aid understanding of the effects of sulfur metabolism on fermentation and the mechanism of microbial adaptation after pH reduction, providing new perspectives on the optimization of fermentation processes.

The bacterial succession and its role in flavor compounds formation during the fermentation of cigar tobacco leaves

Fermentation is the key process required for developing the characteristic properties of cigar tobacco leaves, complex microorganisms are involved in this process. However, the microbial fermentation mechanisms during the fermentation process have not been well-characterized. This study investigated the dynamic changes in conventional chemical composition, flavor compounds, and bacterial community during the fermentation of cigar tobacco leaves from Hainan and Sichuan provinces in China, as well as the potential roles of bacteria. Fermentation resulted in a reduction of conventional chemical components in tobacco leaves, with the exception of a noteworthy increase in insoluble protein content. Furthermore, the levels of 10 organic acids and 19 amino acids showed a significant decrease, whereas the concentration of 30 aromatic substances exhibited a unimodal trend. Before fermentation, the bacterial community structures and dominant bacteria in Hainan and Sichuan tobacco leaves differed significantly. As fermentation progressed, the community structures in the two regions became relatively similar, with Delftia, Ochrobactrum, Rhodococcus, and Stenotrophomonas being dominant. Furthermore, a total of 12 functional bacterial genera were identified in Hainan and Sichuan tobacco leaves using bidirectional orthogonal partial least squares (O2PLS) analysis. Delftia, Ochrobactrum, and Rhodococcus demonstrated a significant negative correlation with oleic acid and linoleic acid, while Stenotrophomonas and Delftia showed a significant negative correlation with undesirable amino acids, such as Ala and Glu. In addition, Bacillus showed a positive correlation with benzaldehyde, while Kocuria displayed a positive correlation with 2-acetylfuran, isophorone, 2, 6-nonadienal, and β-damascenone. The co-occurrence network analysis of microorganisms revealed a prevalence of positive correlations within the bacterial network, with non-abundant bacteria potentially contributing to the stabilization of the bacterial community. These findings can improve the overall tobacco quality and provide a novel perspective on the utilization of microorganisms in the fermentation of cigar tobacco leaves.

Changes in sulfur in soybean rhizosphere soil and the response of microbial flora in a continuous cropping system mediated by Funneliformis mosseae

Soybean is an S-loving crop, and continuous cropping might cause soil sulfur shortage. The primary objectives of this study are to determine whether Funneliformis mosseae (F. mosseae) can enhance the content of available S in S-deficient soil and thereby improve the sulfur utilization rate in soybean. The experiment used Heinong 48 (HN48), a soybean variety with a vast planting area in Heilongjiang Province, and F. mosseae was inoculated in the soil of soybean that had been continuously cropped for 0 and 3 years. The results of the barium sulfur turbidimetric assay show that the sulfur content in the soil and soybean was reduced by continuous cropping and increased by inoculation with F. mosseae; the results of the macro-genome sequencing technology, show that the diversity and abundance of bacteria in the soil was decreased by continuous cropping and increased by inoculation with F. mosseae. The sulfur-oxidizing bacteria (SOB) activity and sulfur-related gene expression levels were lower in the continuous crop group compared to the control group and higher in the F.mosseae-inoculated group compared to the control group. Continuous cropping reduced the sulfur content and ratio of soybean rhizosphere soil, affecting soil flora activity and thus soybean growth; F. mosseae inoculation increased the sulfur content of soybean root-perimeter soil and plants, increased the diversity and abundance of rhizosphere soil microorganisms, increased the expression of genes for sulfur transport systems, sulfur metabolism, and other metabolic functions related to elemental sulfur, and increased the species abundance and metabolic vigor of most SOB. In summary, continuous cropping inhibits soil sulfur uptake and utilization in soybean while the inoculation with F. mosseae can significantly improve this situation. This study offers a theoretical research foundation for using AMF as a bio-fungal agent to enhance soil sulfur use. It also supports the decrease of chemical fertilizers, their substitution, and the protection of native soil.

Short-Term Impact of Recycling-Derived Fertilizers on Their P Supply for Perennial Ryegrass (Lolium perenne)

Various nutrient recycling technologies are currently under development in order to alleviate the dependency of non-renewable raw material for the production of mineral phosphorus fertilizers commonly used in agriculture. The resulting products, such as struvites and ashes, need to be assessed for their application as so-called recycling-derived fertilizers (RDFs) in the agricultural sector prior to commercialization. Here, we conducted a short-term (54 days) trial to investigate the impact of different phosphorus fertilizers on plant growth and the soil P cycling microbiota. Lolium perenne was grown with application of superphosphate (SP) as inorganic fertilizer, two ashes (poultry litter ash (PLA) and sewage sludge ash (SSA)), and two struvites (municipal wastewater struvite (MWS) and commercial CrystalGreen® (CGS)) applied at 20 and 60 kg P ha-1 in four replicates. A P-free control (SP0) was also included in the trial. Struvite application increased plant dry weights, and available P acid phosphatase activity was significantly improved for struvites at the high P application rate. The ash RDFs showed a liming effect at 60 kg P ha-1, and PLA60 negatively affected acid phosphatase activity, while PLA20 had significantly lower phoD copy numbers. P mobilization from phosphonates and phytates was not affected. TCP solubilization was negatively affected by mineral SP fertilizer application at both P concentrations. The bacterial (16S and phoD) communities were only marginally affected by the tested P fertilizers. Overall, struvites appeared to be a suitable substitute for superphosphate fertilization for Irish L. perenne pastures.

Suppressive performance of food waste composting with polylactic acid: Emphasis on microbial core metabolism pathways and mechanism

The aim of this study was to assess the effect of polylactic acid (PLA) on microbial community composition and core metabolism pathways in food waste (FW) composting. The presence of PLA negatively influenced microbial community richness and decreased respectively the abundance of Bacillus, Halocella and Cellvibrio at mesophilic, thermophilic and mature phases. Analysis of microbial metabolism at the gene level help to understand the mechanism in co-composting with FW and PLA. The expression of core functional genes related to lactide metabolism was stimulated by PLA degradation at thermophilic and mature phases. The sum of absolute abundance of functional genes that involved in first and second carbon oxidation of tricarboxylic acid cycle was decreased due to the existence of PLA. The transformation between 2-Oxoglutarate and Succinyl-CoA were interfered in thermophilic phase, which might result in the lower germination index in PLA group (115%) than that in control (186%).

Microbiome - based agents can optimize composting of agricultural wastes by modifying microbial communities

Microorganisms that facilitate the decomposition of agricultural wastes are of importance during composting processes. Here, we assessed if microbial agents, comprising Clonostachys rosea, Bacillus amylolyticus and Rhodospirillum photometricum can facilitate the decomposition of a compost mix of vegetable waste, chicken manure, sawdust, and biochar. The results showed that inoculating the compost mix with the microbial agents elevated the compost temperature, increased the thermophilic period, and enhanced cellulose degradation. Microbial agent inoculation also changed the diversity and richness of decomposing microbial communities. Among the microbial agents, the mixture of C. rosea and B. amylolyticus performed better than other mixtures. Taken together, the results confirmed that the microbial agents comprising C. rosea can enhance the composting process by ameliorating the physiochemical conditions of agricultural wastes and promoting the diversity and proliferation of beneficial bacteria involved in the decomposition of cellulose.

Dissolved organic matter evolution can reflect the maturity of compost: Insight into common composting technology and material composition

Dissolved organic matter (DOM) can clearly reflect composting components changes, thus it is supposed to indicate the humification process during composting. To demonstrate this, three compost mixtures and two techniques were arranged. DOM evolution was detected by three spectral techniques. X-ray diffraction (XRD) showed that the crystal structure substances decreased gradually during the composting, including cellulose, struvite, sylvine, quartz, and calcite; Specifically, the struvite was found, which was conducive to the fixation of nitrogen and phosphorus. Fourier transform infrared spectroscopy (FTIR) and three-dimensional fluorescence spectroscopy (3D-EEM) further showed that pig manure-based mixtures, added cabbage, and windrow composting are beneficial to sugar, protein, fulvic acid, and soluble microbial by-products decompose and humic acids produce. This process was closely related to the change of physical-chemical parameters (temperature; pH; moisture content; and NH₄⁺-N content) and maturity index (C/N ratio, E₄/E₆ and GI). Therefore, DOM evolution could quickly reflect the maturity process of compost. In subsequent research, the quantitative analysis of DOM components can be considered to modify DOM spectral parameters, or to build a model, so as to achieve rapid evaluation of compost maturity.

Exploring the mechanism associated with methane emissions during composting: Inoculation with lignocellulose-degrading microorganisms

Inoculation with microorganisms is an effective strategy for improving traditional composting processes. This study explored the effects of inoculation with lignocellulose-degrading microorganisms (LDM) on the degradation of organic matter (OM), methane (CH₄) emissions, and the microbial community (bacteria and methanogens) during composting. The results showed that LDM accelerated the degradation of OM (including the lignocellulose fraction) and increased the CH₄ releases in the later thermophilic and cooling stages during composting. At the ending of composting, LDM increased the CH₄ emissions by 38.6% compared with the control. Moreover, LDM significantly increased the abundances of members of the bacterial and methanogenic community during the later thermophilic period (P < 0.05). In addition, LDM promoted the growth and activity of major bacterial genera (e.g., Ureibacillus) with the ability to degrade macromolecular OM, as well as affecting key methanogens (e.g., Methanocorpusculum) in the composting system. Network analysis and variance partitioning analysis indicated that OM and temperature were the main factors that affected the bacterial and methanogen community structures. Structural equation modeling demonstrated that the higher CH₄ emissions under LDM were related to the growth of methanogens, which was facilitated by the anaerobic environment produced by large amounts of CO₂. Thus, aerobic conditions should be improved during the end of the thermophilic and cooling composting period when inoculating with lignocellulose-degrading microorganisms in order to reduce CH₄ emissions.

Fate of antibiotic resistance genes in cultivation substrate and its association with bacterial communities throughout commercial production of Agaricus bisporus

Animal manure is an important raw material for Agaricus bisporus production; however, it is also a reservoir for antibiotic residues, antibiotic resistance genes (ARGs), and antibiotic-resistant bacteria. Little is known about the influence of the commercial cultivation of A. bisporus on the dynamics of ARGs and the underlying mechanisms that cause their variations. In this study, we investigated the fate of 285 ARGs, 10 mobile genetic elements, and seven major categories of antibiotic residues in substrate and mushroom samples at different production phases. The results showed that commercial substrate preparation, particularly the pasteurization phase, was highly efficient in removing ARGs from the substrate. We further found that mycelium proliferation of A. bisporus contributed significantly to the removal of ARGs from the substrate and casing soil. The bacterial community is the key driver of changes in ARGs during the commercial cultivation of A. bisporus, which explained 46.67% of the variation in ARGs. Our results indicate that, despite the addition of animal manure, the risk of ARG dissemination to fruiting bodies and the environment is low. We propose that bioremediation by specific edible fungi might be a novel and promising method for scavenging antimicrobial resistance contamination from soil environment.

Effect of microbial agents on maturity, humification, and stability and the bacterial succession of spent mushroom substrate composting

Two composting experiments were conducted to investigate the effects of commercial microbial agents on microbial succession and nutrient flow such as humification, maturation, and stability during the aerobic composting of the spent mushroom substrate (SMS). The cellulose degradation rate of T (added microbial agents at the initial stage) reached 41.8%, which was much significantly (p < 0.05) higher than that of CK (14.9%). The seed germination index (GI) in T (82.38%) was significantly (p < 0.05) higher than that in CK (74.74%) in the maturation phase. Moreover, the total organic carbon/total nitrogen ratio (C/N) and electrical conductivity (EC) value of T decreased to 10.5 and 2.37 mS/cm, respectively. Chemical detection and fluorescence excitation-emission region integration method (EEM-FRI) analysis showed that the microbial agents significantly accelerated the organic matter (OM) decomposition and promoted the quality of mature compost using SMS as a single raw material. The bacterial abundance of T was significantly richer than the CK due to the addition of microbial agents. The results could provide a comprehensive understanding of adding microbial agents into composting SMS and a scientific feasibility strategy to rational utilization of resources in the edible fungi industry, which was conducive to the waste management and sustainable development of the edible fungi industry.

Phytotoxicity of farm livestock manures in facultative heap composting using the seed germination index as indicator

Static facultative heap composting of animal manure is widely used in China, but there is almost no systematic research on the phytotoxicity of the produced compost. Here, we evaluated the phytotoxic variation in compost produced by facultative heap composting of four types of animal manure (chicken manure, pig manure, sheep manure, and cattle manure) using different plant seeds (cucumber, radish, Chinese cabbage, and oilseed rape) to determine germination index (GI). The key factors that affected GI values were identified, including the dynamics of the phytotoxicity and microbial community during heap composting. Sensitivity to toxicity differed depending on the type of plant seed used. Phytotoxicity during facultative heap composting, evaluated by the GI, was in the order: chicken manure (0-6.6 %) < pig manure (14.4-90.5 %) < sheep manure (46.0-93.0 %) < cattle manure (50.2-105.8 %). Network analysis showed that the volatile fatty acid (VFA) concentration was positively correlated with Firmicutes abundance, and NH₄⁺-N was correlated with Actinobacteria, Proteobacteria, and Bacteroidetes. More bacteria were stimulated to participate in conversions of dissolved organic carbon, dissolved nitrogen, VFA, and ammonia-nitrogen (NH₄⁺-N) in sheep manure heap composting than that in other manure. The GI was most affected by VFA in chicken manure and cattle manure heap composting, while NH₄⁺-N was the main factor affecting the GI in pig manure and sheep manure compost. The dissolved carbon and nitrogen content and composition, as well as the core and proprietary microbial communities, were the primary factors that affected the succession of phytotoxic substances in facultative heap composting, which in turn affected GI values. In this study, the key pathways of livestock manure composting that affected GI and phytotoxicity were found and evaluated, which provided new insights and theoretical support for the safe use of organic fertilizer.

Impacts of composting duration on physicochemical properties and microbial communities during short-term composting for the substrate for oyster mushrooms

A short-term composting process to prepare substrate is an effective way to cultivate oyster mushrooms (Pleurotus spp.), which can increase the yield of mushrooms and lower the rate of contamination in non-industrialized cultivation. Moreover, it is different from the traditional composting processes for fertilizers and lacks systematic study, such as microbial succession and compost quality. In this study, a series of different tests of composting duration (0, 2, 4 and 5 d) were performed. A composting duration of 4-5 d over 58 °C was suitable for mushroom cultivation based on the biological efficiency (BE) range of 69.76-73.41 % and the contamination rate of 0 %. The content of total carbon (TC) continuously decreased during composting, while the content of total nitrogen (TN) reacted in an opposite matter. The final TN and C/N ratios were 1.89 % and 28/1, respectively, which fell well within the optimal range of nutritional requirements for oyster mushroom cultivation. The composting bacteria were more diverse than the fungal species. Caldibacillus, Thermobispora, Thermopolyspora, Thermobacillus and Ureibacillus were the predominant bacterial genera during the thermophilic stage. Co-occurrence patterns of microbial communities and physicochemical properties were performed using a network analysis, which indicated that bacteria can play more efficient roles than fungi in the degradation of organic matter. The structural equation model showed that composting duration significantly affected bacterial diversity, lignocellulose degradation rates, and BE. The correlations between bioinformatics parameters with composting characters and agronomic traits were determined by the Mantel test and showed that the induction of bacterial diversity over time rapidly activated carbon metabolism during short-term composting. This study provides a new idea of agro-waste composting for mushroom cultivation.

Evaluation of key microbial community succession and enzyme activities of nitrogen transformation in pig manure composting process through multi angle analysis

This experiment aimed to investigate changes in enzyme activity, microbial succession, and nitrogen conversion caused by different initial carbon-to-nitrogen ratios of 25:1, 35:1 and 20:1 (namely CK, T1 and T2) during pig manure composting. The results showed that the lower carbon-to-nitrogen ratio (T2) after composting retained 19.64 g/kg of TN which was more than 16.74 and 17.32 g/kg in treatments of CK and T1, respectively, but excessive conversion of ammonium nitrogen to ammonia gas resulted in nitrogen loss. Additional straw in T1 could play the role as a bulking agent. After composting, TN in T1 retained the most, and TN contents were 63.51 %, 67.34 % and 56.24 % in CK, T1 and T2, respectively. Network analysis indicated that many types of microorganisms functioned as a whole community at various stages of nitrogen cycle. This study suggests that microbial community structure modification might be a good strategy to reduce ammonium nitrogen loss.

Recent trends and advances in composting and vermicomposting technologies: A review

Composting technologies have come a long way, developing from static heaps and windrow composting to smart, artificial intelligence-assisted reactor composting. While in previous years, much attention has been paid to identifying ideal organic waste streams and suitable co-composting candidates, more recent efforts tried to determine novel process-enhancing supplements. These include various single and mixed microbial cultures, additives, bulking agents, or combinations thereof. However, there is still ample need to fine-tune the composting process in order to reduce its impact on the environment and streamline it with circular economy goals. In this review, we highlight recent advances in integrating mathematical modelling, novel supplements, and reactor designs with (vermi-) composting practices and provide an outlook for future developments. These results should serve as reference point to target adjusting screws for process improvement and provide a guideline for waste management officials and stakeholders.

Effects of di-n-butyl phthalate on aerobic composting process of agricultural waste: Mainly based on bacterial biomass and community dynamics analysis

Phthalic acid esters (PAEs) pollution has become a major environmental problem in agricultural waste composting. However, little information was available about the how the PAEs alter microbial processes during composting. This study investigated the effects of di-n-butyl phthalate (DBP) on bacterial biomass and community dynamics during composting. The results showed that a decreasing of DBP was observed from thermophilic phase and 43.26% of DBP was degraded after composting. The bacterial biomass and diversity during composting were reduced under DBP stress, so delaying the decomposition of organic matter. Moreover, the changes in bacterial community were observed since the thermophilic phase of DBP-contaminated composting. KEGG pathway analysis indicated that DBP stress decreased the relative abundance of the main metabolic pathways and inhibited compost maturation. Moreover, DBP stress had more significant correlation with the dominant bacteria. This work will expand the understanding of PAEs-contaminated organic waste composting and further control of PAEs pollutants.

Aerobic composting of chicken manure with amoxicillin: Alpha diversity is closely related to lipid metabolism, and two-component systems mediating their relationship

Composting is a technology that can use various functional microorganisms to degrade antibiotics. However, antibiotics will cause a coercion for the growth of most microorganisms. Microorganism can survive different environments, thanks to the development of different adaptive responses. Often, two-component systems sense changes in the environment and trigger a cellular response and adaptation. Therefore, the main purpose of this study was to explore how the two-component system modulates the corresponding metabolic functions to affect alpha diversity during composting. The results show that amoxicillin increases species diversity, reduces species richness. Lipid metabolism is an important metabolic pathway mediating changes in alpha diversity. Two-component system indirectly affects alpha diversity by regulating lipid metabolism. Firmicutes are important microbial communities mediating changes in alpha diversity This work presents an understanding of the impact of environmental information processing on microbial diversity, during composting.

Composting temperature directly affects the removal of antibiotic resistance genes and mobile genetic elements in livestock manure

The high antibiotic resistance gene (ARGs) contents in livestock manure pose a potential risk to environment and human health. The heap composting with an ambient temperature and thermophilic composting are two methods for converting livestock manure into fertilizer. This study investigated the variations in ARGs and mobile genetic elements (MGEs) and revealed potential mechanisms for ARGs removal using the two composting methods. The ARGs abundance were enriched by 44-fold in heap composting, among them, the macrolide-resistance genes increased significantly. On the contrary, the ARGs were removed by 92% in thermophilic composting, among them, tetracycline-resistance genes decreased by 97%. The bacterial hosts of ARGs were associated with the variations of ARGs and MGEs. The tetO was correlated with the most diverse bacteria in heap composting, and Bacteroidetes was the major host bacteria. While tetT was correlated with the most diverse bacteria in thermophilic composting, and Proteobacteria was the major host bacteria. Structural equation models showed that the enrichment of ARGs in heap composting was mainly correlated with bacterial communities, whereas, the removal of ARGs in thermophilic composting was directly affect by MGEs. Composting temperature directly affected the variations in ARGs. Higher and lower temperatures significantly decreased and increased, respectively, ARGs and MGEs abundance levels.

Comparison between cold plasma, ultrasonication, and alkaline hydrogen peroxide pretreatments of garden waste to enhance humification in subsequent composting with kitchen waste: Performance and mechanisms

This study compared the performance and mechanisms of cold plasma, ultrasonication, and alkali-assisted hydrogen peroxide for garden waste pretreatment to advance humification in composting with kitchen waste. High-throughput sequencing integrated with Functional Annotation of Prokaryotic Taxa was used to relate bacterial dynamics to humification. Results show that all pretreatment techniques accelerated humification by 37.5% - 45.7% during composting in comparison to the control treatment. Ultrasonication and alkalization preferred to decompose lignocellulose to produce humus precursors in garden waste, thereby facilitating humus formation at the beginning of composting. By contrast, cold plasma was much faster and simpler than other pretreatment techniques to effectively disrupt the surface structure and reduce the crystallinity of garden waste to enrich functional bacteria for aerobic chemoheterotrophy, xylanolysis, cellulolysis, and ligninolysis during composting. As such, a more robust bacterial community was developed after cold plasma pretreatment to advance humification at the mature stage of composting.

Clarification of the Dynamic Autothermal Thermophilic Aerobic Digestion Process Using Metagenomic Analysis

This study details a unique process of autothermal thermophilic aerobic digestion (ATAD) of human excreta useful in producing nitrogen-rich and pathogen-free organic fertilizer. The process was divided into initial, middle, and final phases, based on changes in temperature, dissolved oxygen (DO), and bacterial community structure. The aim of this study was to determine bacterial factors that would affect liquid fertilizer production in the process, using shotgun metagenomic analysis of each phase. Although the abundances of all 28 gene categories include 4 categories in SEED subsystems level 1 were similar to those in another type of wastewater treatment system, the abundances of 4 gene categories changed remarkably. Among them, a decrease in the abundance of the phage-related gene category and the presence of antibacterial substances in secondary metabolism may explain the change in bacterial community structure from the material to the initial phase. Increases in the abundances of two gene categories, phage-related and secondary metabolism, coincided with a decrease in alpha diversity from the material to the initial phase. A potential increase in the abundance of genes in the category of sporulation from the middle to the final phase was correlated with deterioration of growth conditions and stabilization processes. In addition, prompt consumption of short-chain fatty acids in the initial phase and unusually stable ammonia accumulation throughout the process could be explained by the presence/absence of related metabolic genes. In conclusion, the relationships between bacterial function and unique characteristics of ATAD were revealed; our findings support the enhancement of liquid fertilizer production from wastewater.

IMPORTANCE Metagenome analysis was performed to determine the microbial dynamics of the unique autothermal thermophilic aerobic digestion process of human excreta, which includes initial, middle, and final phases. In this study, we revealed the details of functional genes related to physicochemical and bacterial characteristics in the ATAD process. Four gene categories showed increases and decreases during the digestion process. In addition, the unusual stable accumulation of ammonia and prompt consumption of short-chain fatty acids were explained by the absence or presence of related metabolic genes. In addition to revealing the relationships between bacteria and physicochemical properties, the results of this research may support improving wastewater management systems worldwide by using the ATAD process in liquid fertilizer production systems.

Key factors affecting seed germination in phytotoxicity tests during sheep manure composting with carbon additives

The germination index (GI) was widely applied to evaluate the phytotoxicity of compost. This study investigated the key phytotoxicity factors affecting seed germination in compost by using aqueous extracts in seed germination tests. The relationship between water-soluble substances in compost and seed germination, and their association with the microbial community were identified. In this study, sheep manure (SM) composted along or with three carbon additives (mushroom substrate, MS; cornstalks, CS; garden substrate, GS) for 49 days and, during this time, changes in multiple physical-chemical parameters, carbon and nitrogen matters, germination indexes (GI) and the compost microbiome were monitored. The results showed that all additives decreased water-soluble total nitrogen (TN), ammonium nitrogen (NH₄⁺-N) and low molecular weight organic acids, and significantly improved the seed germination indexes (seed germination rate, radical length and GI). The GI was correlated with water-soluble carbon degradation products (TOC, butyric acid, humic acid) and certain bacteria (Planifilum, Oceanobacillus, Ruminococcaceae_UCG_005 and Saccharomonospora). A structural equation model revealed that the main factors affecting seed germination were TOC (SM compost), acetic acid (SM+MS compost), humic acid (SM+CS compost), and pH (SM+GS compost). Low TOC and low molecular weight organic acids contents and higher humic acid content promoted GI. The research results could provide theoretical basis and measures for directional regulation of compost maturity.